Eric Banks 23c6aee236 Added in some basic unit tests for polyploid consensus creation in RR. ... - Uncovered small bug in the fix that I added yesterday, which is now fixed properly. - Uncovered massive general bug: polyploid consensus is totally busted for deletions (because of call to read.getReadBases()[readPos]). - Need to consult Mauricio on what to do here (are we supporting het compression for deletions? (Insertions are definitely not supported)		2013-02-05 10:35:45 -05:00
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annotator	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	Update MD5s to reflect version number change in the BAM header	2013-02-01 13:51:31 -05:00
compression/reducereads	Added in some basic unit tests for polyploid consensus creation in RR.	2013-02-05 10:35:45 -05:00
diagnostics	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
diffengine	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
genotyper	Apparently I'm a failure at rebasing...there should have been only one commit message to write. But whatever, here it is again:	2013-02-04 14:16:28 -05:00
haplotypecaller	Added some docs, unit test, and contracts to SimpleDeBruijnAssembler.	2013-02-04 15:17:22 -05:00
indels	Update MD5s to reflect version number change in the BAM header	2013-02-01 13:51:31 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
variantutils	Move BaseUtils back to the GATK by request, along with associated utility methods	2013-01-30 13:09:44 -05:00